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Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Open accessAbstract
Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis . The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nearly one-fifth of the genes of the ancestor are eumetazoan novelties in the sense that they have no recognizable homologs outside of animals, or contain new protein domains and/or domain combinations that are not found in other eukaryotes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
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In the paper
“The anemone genome is surprisingly complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
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In the paper
“In contrast, only 33 genes are found in Nematostella and both Drosophila and C. elegans but not in any vertebrate, representing putative deuterostome or vertebrate loss, indicating a much lower degree of gene loss in the vertebrates than in the ecdysozoan model systems.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“Surprisingly, the human genome has many more such orthologous pairs with Nematostella (6,989) than with nonvertebrate bilaterians, including Drosophila (5,772), C. elegans (4,846), and even the invertebrate chordate Ciona intestinalis (6,313).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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“Combining homology-based and ab initio methods with sequences from over 146,000 expressed sequence tags, we predicted ~27,000 complete or partial protein-coding transcripts in the genome (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
What the sources say
- Not checked yetcites [32]
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“After correcting for sampling, we estimated that each pair of haplotypes differ at 0.65% of nucleotide positions (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
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“Althought many eumetazoan introns are evidently of ancient eukaryotic origin (46) --for example, nearly 26% of human and Nematostella introns are conserved with Arabidopsis, and 24% with Cryptococcus --the remainder appear to be shared only by animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [46] source
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In the paper
“Of the 7,766 ancestral eumetazoan gene families, only 72% (5,626) are represented in the complete genomes of all three major modern eumetazoan lineages: cnidarians (i.e., Nematostella), protostomes (i.e., Drosophila and/or C. elegans), and deuterostomes (requiring presence of at least two of pufferfish, frog, and human).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“To approximate the gene repertoire of the eumetazoan ancestor we constructed 7,766 putatively orthologous gene families that are anchored by reciprocal best-scoring BLAST alignments between genes from anemone and one or more of fly, nematode, human, frog, or fish [S].”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“Over 500 families of them were discovered in the genome, including DNA transposons and both LTR and non-LTR retrotransposons (Table S2.3).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
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In the paper
“Metaphase spreads indicate a diploid chromosome number of 2N=30 (Fig S2.4).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
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In the paper
“Long branch lengths, indicating increased levels of sequence divergence, were found along the fly, nematode, and sea squirt lineages.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
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In the paper
“The typical locus in the draft genome is in a contiguous gap-free stretch of nearly 20 Kb.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
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In the paper
“The sea anemone sequences, however, appear to be evolving at a rate comparable to, or even somewhat lower than, vertebrates.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
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In the paper
“As expected, the two cnidarians Nematostella and Hydra form a monophyletic group that branched off the metazoan stem prior to the radiation of bilaterians.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
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In the paper
“More than 12,000 of these are found in robust eumetazoan gene families, and are therefore supported as orthologs of genes in other animals (see below).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
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In the paper
“More than 25% of the genome is made of repetitive elements that are fossilized copies of transposable elements.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“Figure 3b shows intron gain (left) and loss (right) events inferred by weighted parsimony analysis of 2,645 intron positions that lie within highly conserved protein sequence in two or more animals, the flowering plant Arabidopsis, and the relatively intron-rich fungus Cryptococcus neoformans (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [32]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Slightly more than 10% of the EST contigs have significant (95% identify, 75% length) alignments to multiple scaffolds (32), providing an estimate of the redundancy of the assembly, which appears to arise from the occasional separate assembly of divergent haplotypes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
What the sources say
- Not checked yetcites [32]
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In the paper
“nearly 750 million years later, are still maintained in modern vertebrates”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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In the paper
“Within animals, intron gains range from 8-22% relative to the content of the eumetazoan ancestor.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
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In the paper
“others such as nidogen are novel pairings of ancient domains (Figure 5c)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“the LIM-homeobox transcription factors are the result of a fusion of the ancient LIM protein-protein interaction and homeobox DNA-binding domains on the eumetazoan stem”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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In the paper
“Matrix metalloproteases also were invented as Type II novelties”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“These segments span 89% of the base pairs of the human genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“some, such as tolloid are novel pairings of ancient domains (Type III)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Fyn itself is a more recent invention derived on the tetrapod stem by gene duplication”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Within each segment, however, local gene order is considerably scrambled.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“genes with neuronal activities are abundant among its novelties”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Eumetazoan networks and pathways
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“To remove confounding signals from recent rearrangements, we used comparisons with the genomes of other chordates to identify 98 human segments large enough that they each contain descendants of 40 or more ancestral eumetazoan genes, that do not appear to have undergone recent breaks or fusions (Figures 4a, S7.1) (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [32]
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In the paper
“guidance cues such as netrin and semaphorin that mediate adhesion are novelties with no clear homology to ancient eukaryotic proteins”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“We find that in both pathways, the secreted ligands and their antagonists (wnt, SFRP, BMP, chordin etc.) are novelties (Figure 5b)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“genes known to be involved in mesoderm development in bilaterians are also enriched among eumetazoan novelties”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Eumetazoan networks and pathways
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In the paper
“Transcription factors that are activated downstream of Wnt signaling are ancient”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Type I receptors of the TGFbeta pathway arose as a pairing of novel animal domains with ancient domains (Type II novelties)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“An ancestral linkage group of particular interest includes the eumetazoan Hox cluster of homeobox transcription factors that regulate anterior-posterior identity in bilaterians.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“we find the novel genes to be significantly enriched for signal transduction, cell communication and adhesion, and developmental processes (32)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Eumetazoan networks and pathways
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of the 4,402 ancestral eumetazoan gene families represented in the largest anemone scaffolds and human segments (i.e., in the genomic regions large enough to permit statistically significant analysis, and therefore eligible for consideration in our analysis), more than 30% (1,336) participate in a conserved linkage group.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“The complete Oxford grid showing all 13 PALs is shown in Table S7.2.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“In contrast to intron gains, which seem to occur more or less uniformly across animal phyla, some lineages appear to have experienced significant intron loss, notably fly, nematode, and sea squirt, which have each discarded 50-90% of inferred ancestral eumetazoan introns.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
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In the paper
“but the ones involved in TGF-beta signaling are novel”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Basement membrane proteins such as collagen and laminin arose as Type II novelties along the stem leading to the Eumetazoa”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“they had already duplicated and diversified on the eumetazoan stem to establish the subfamilies”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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In the paper
“The receptor in the Wnt pathway, frizzled, also arose as a Type I eumetazoan novelty”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“some are Type II novelties (dickkopf)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“Nearly 80% (6,182/7,766) of the ancestral eumetazoan genes have clearly identifiable relatives (i.e., proteins with significant sequence homology and conserved domain architecture) outside of the animals, including fungi, plants, slime molds, ciliates, or other species available from public datasets (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
What the sources say
- Not checked yetcites [32]
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In the paper
“not only were these genes present in the eumetazoan ancestor”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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In the paper
“Notch proteins have two Notch domains found only in metazoans in addition to ancient eukaryotic ankyrin and EGF domains”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“A more sensitive approach can assign more than twice as many ancestral genes to a PAL (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“as well as the core gene set required to execute sophisticated neural and muscular function”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
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In the paper
“In terms of their bulk contribution to the genome size, DNA transposons are fourfold more abundant than retrotransposons (Table S2.3).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“their 5'-CACAG termini differ from the 5'-CACTA termini of the plant transposons.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We were able to assign one or more PFAM domains to 15,102 human genes and 12,202 Nematostella genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
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In the paper
“Only nine ortholog sets contained one gene from each of the twelve whole genomes plus a Mnemiopsis sequence.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
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In the paper
“Adding up these expected numbers gives us an estimate of 18,345 bona fide Nematostella genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
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In the paper
“Representatives of all reported superfamilies and groups of eukaryotic DNA transposons (14-16), excluding the Transib superfamily and the Mariner group of the Mariner superfamily, are present in the anemone genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
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In the paper
“Other sarcomere proteins are Type II novelties (e.g.nebulin and tropomodulin)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
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In the paper
“it was intron rich”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
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In the paper
“the sea anemone genome, in addition to the canonical hAT transposons contains two novel groups, hAT5 and hAT6, characterized by 5-and 6-bp TSDs, respectively.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“their ORFs coding for transposases, reverse transcriptases, and other transposon-specific proteins are not severely damaged by mutations.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“different classes of autonomous DNA transposons are represented by just a few families.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“These families are composed of a small number of copies (from 1 to ~5,000)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“This type of reversal does not appear in human-Drosophila, human-Caenorhabditis , or Drosophila-Caenorhabditis comparisons (data not shown).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
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In the paper
“16 Pfam domains previously exclusively found only in vertebrates, but not in other phyla of bilateria (or other eukaryotes), are present in Nematostella genome, including:”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
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In the paper
“some are parings of old domains with novel animalspecific domains (such as Dsh, Arx, neuralized)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
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In the paper
“Of the PFAM domains present in human, mouse, dog, chicken, frog and fugu, Nematostella has more in common than any of Ciona, fruit fly, or nematode.(Figure S3.4)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
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In the paper
“By this method, 337 ortholog sets were identified that had one gene representing each of the twelve whole genome datasets.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
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In the paper
“In general, the gene families showing strong expansions along the two lineages are different.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
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In the paper
“A similar algorithm applied to the ENSEMBL annotation of the human genome detected 504 recent expansions with 1,317 genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
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In the paper
“using reverse transcriptase/integrase and transposase encoded by the anemone Troyka, hAT5, and hAT6 transposons as queries in TBLASTN searches against GenBank DNA sequences, we found that proteins closest to the queries (>30% protein identity) are encoded by TEs characterized by the same unusual lengths of TSDs.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Numerous genes known to be involved in neurogenesis, such as members of the homeobox and basic helixloop helix transcription factor families (Emx, Otp, Otx; achaete-scute), can be traced to ancient eukaryotic genes with these signature domains”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
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In the paper
“The human genome has more genes with a mutual best hit in Nematostella than in the proteomes of Ciona, fruit flies or nematodes.(Figure S3.2)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
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In the paper
“The eumetazoan ancestor possessed over fifteen hundred genes that are apparently novel relative to other eukaryotic kingdoms”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
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“Over 3% of the anemone genome is made of fossilized copies of self-synthesized Polinton DNA transposons whose transposition depends on the Polinton-encoded DNA polymerase and integrase (17).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [17] source
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In the paper
“different classes of anemone retrotransposons, including Gypsy, DIRS, Penelope, and CR1, are composed of more than 50-100 families each”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“Various components of the dystrophin-associated protein complex (DPC) in the sarcolemma such as dystrophin, syntrophin, beta-dystrobrevin and beta-sarcoglycan are Type I novelties”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
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In the paper
“Hence, in Nematostella, there is no evidence for recent selection for retention of new genes greated by tandem duplication with PF000001.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes- The authors state this as an assumption: Any gene has an equal probability of getting duplicated and fixed in the population.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“a significant number of animal-specific genes contain sequences with no readily recognizable counterparts outside of animals”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
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In the paper
“In the human genome, on the other hand, 112 such genes are observed, with an expected value of 29 +-5.3, consistent with a strong recent selective retention of such receptors (olfactory and visual) within vertebrates or mammals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- The authors state this as an assumption: Any gene has an equal probability of getting duplicated and fixed in the population.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the ancestor had blocks of linked genes that remain together in the modern human and anemone genomes”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“the anemone genome harbors two families of Tx1-like non-LTR retrotransposons, Tx1-1_NV and Tx1-2_NV, inserted in 5S rRNA and U2 smRNA, respectively, at target sites identical to those of different Tx1 elements in fish (18), frog and lancelet.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [18] source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Following identification of the IS4EU TEs in the anemone genome, members of this superfamily have been also found in other species, including lancelet.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“Troyka, a novel type of LTR retrotransposons distantly related to the Gypsy superfamily, is characterized by 3-bp target site duplications (TSDs)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“We compared predicted protein sequences from Nematostella to those from other metazoan and outgroup genomes, and find that Nematostella genes are more similar to vertebrate genes than to fly and nematode genes using bayesian branch length estimation and an analysis of percent sequence identity.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
What the sources say
- Not checked yetcites [31] source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“elements from the oldest families are less than 15% divergent from their consensus sequences”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Some are the result of domain shuffling, bringing together on the animal stem new combinations of domains that are shared with other eukaryotes”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
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In the paper
“Of the 7,766 ancestral metaozan gene clusters, 1,619 are composed of a single gene from each of the six representative metazoan genomes listed in Supplement S4: human, fish, frog, Nematostella, fruit fly and nematode.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Even, En/Spm (also called CACTA) and transposons, which were believed to populate plants genomes only (14), reside in the anemone genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14] source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The Nematostella genome contains many protines with domain architectures (combinations of PFAM domains) that are shared exclusively with vertebrate genes.(Figure S3.3)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
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In the paper
“the results of the sampling indicate that about one third of all genes in the FM1.0 set could be expected to be rejected by manual reviews.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“This clustering of scaffolds and chromosome segments defines 15 large PALs, each with descendants of more than one hundred ancestral eumetazoan genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > A clustering method allows more extensive reconstruction of putative ancestral linkage groups.
What the sources say
- Not checked yetcites [41] source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Despite early divergence, sea anemone shares more hits with human, than other bilaterians, except vertebrates.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
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In the paper
“In 1,523 of these clusters, the human gene had a mutual best hit to a Nematostella gene, forming clusters of four orthologous genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
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In the paper
“we identified 98 segments of the human genome which appear to be uninterrupted by inter-chromosomal translocations or fusions when compared to the genomes of other chordates.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
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In the paper
“9,947 highly reliable intron splice sites were identified by these requirements.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We next identified 2,347 clusters of orthologous genes in all bilaterian orthologous clusters with an unambiguous 1:1:1 member relationship in human, Drosophila melanogaster (fly), and C. elegans.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
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In the paper
“Having demonstrated that there is extensive conservation of linkage relationships among genes using the conservative statistical criteria described above”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > A clustering method allows more extensive reconstruction of putative ancestral linkage groups.
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“2264 Pfam domains present in all 6 vertebrates with known genomes:human, mouse, dog, chicken, frog and fugu.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
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In the paper
“4342 introns from the seven genomes at 2645 aligned positions which contain an intron in at least one of the seven orthologs.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
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In the paper
“Panther ontology annotations of the inferred ancestral gene set have been tested for enrichment in each of the three categories of novelty (novel sequence, novel domain, and novel combination of domains), as described in section S8, and significant over-and under-representations have been tabulated here”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
What the sources say
- Not checked yetcites [42]
- Not checked yetcites [43] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“4,951 highly reliable introns were identified by these requirements.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Calpain, a protease that regulates the aggregation of Talin, Paxillin and FAK around the receptor appears as a novel domain combination of ancient domains.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Focal adhesion kinase (FAK) is a cytosolic component that appears as a Type II novelty in eumetazoans”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Remarkably, about 81% of the human introns (4,403 of 5,435) are shared with nematostella.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“3055 ancestral genes, or 40% of the ancestral genes are assigned to one of these PALs.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > A clustering method allows more extensive reconstruction of putative ancestral linkage groups.
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Figure S3.4: 2264 Pfam domains present in all 6 vertebrates”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“28.6% of all introns shared by human and Nematostella (and hence present in their LCA) are also shared by Arabidopsis.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results imply that the genome of the eumetazoan ancestor was similarly complex, and that fly and nematode genomes have been modified via sequence divergence, gene and intron loss, and genomic rearrangement.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results imply that the genome of the eumetazoan ancestor was similarly complex, and that fly and nematode genomes have been modified via sequence divergence, gene and intron loss, and genomic rearrangement.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Subsequent diversification in the cnidarian and bilaterian lineages was therefore associated with new regulatory linkages and higher-level integration of these preexisting pathways and networks.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Yet we can infer many of its characteristics --flagellated sperm, development through a process of gastrulation, multiple germ layers, true epithelia lying upon a basement membrane, a lined gut (enteron), a neuromuscular system, multiple sensory systems, and fixed body axes --since they are conserved features retained by its modern descendants.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results strongly suggest that many genes and gene families previously assumed to be chordate or vertebrate innovations are actually much more ancient, and conversely that the fruit fly, soil nematode, and sea squirt lineages have experienced higher levels of divergence and gene loss than Nematostella, consistent with phylogenetic the analysis described below.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This surprising similarity between Nematostella and vertebrates is a recurring theme of our analysis, indicating that both the anemone and vertebrate genomes retain more ancestral eumetazoan features than sequences from flies and nematodes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Our dataset thus nominally contains up to four haplotypes at each locus.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Our reconstructed ancestral gene set is necessarily incomplete since we cannot capture genes that were present in the eumetazoan progenitor but became highly diverged or lost in one or more descendents, nevertheless it provides a starting point for further analysis.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Note that although fungi and animals are phylogenetically closer to each other than either group is to plants, fungi are not by themselves a sufficient outgroup for characterizing the history of eumetazoan introns, since there are putative ancient eukaryotic introns shared by modern animals and plants that have evidently been lost in fungi (46).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [46] source
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“While accelerated rates of molecular evolution have been documented in flies and echinoderms (43) relative to vertebrates, our analysis does not support the extrapolation of these higher rates to all invertebrates.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [43] source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that this analysis is protected from the effects of gene modeling artifacts, since erroneous predictions in the vicinity of splice sites would disrupt alignment, thereby removing such sequences from consideration.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus from a genomic perspective, the eumetazoan ancestor more closely resembled modern vertebrates and anemones.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Comparison of the assembled sequence with open reading frames derived from expressed sequence tags (ESTs, see below) shows that the assembly captures ~95% of the known protein coding content (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
Strength:plain· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesNone of the sources cited for this claim have been checked yet.
In the paper
“The expression domains occur with apparent bilaterial symmetry, i.e., reflecting distinct directed axes both along and perpendicular to the main body axis, and with a left-right plane of symmetry (27)(28)(29).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results strongly suggest that many genes and gene families previously assumed to be chordate or vertebrate innovations are actually much more ancient, and conversely that the fruit fly, soil nematode, and sea squirt lineages have experienced higher levels of divergence and gene loss than Nematostella, consistent with phylogenetic the analysis described below.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These are the most ancient conserved linkages known outside of prokaryotic operons.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Nematostella, however, is not a true broadcast spawner, since while males release sperm into the water, females lay tens to hundreds of eggs encased in a jelly mass that becomes fixed to a benthic substrate.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesNone of the sources cited for this claim have been checked yet.
In the paper
“Using our branch lengths, a very crude molecular clock interpolation based on the eukaryotic time scales of Douzery et al. (42) suggests that the eumetazoan ancestor lived ~670-820 Mya (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [42]
- Not checked yetcites [32]
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes- Rests on an assumption: The rate of protein evolution was constant on the eumetazoan stem for the molecular clock estimate.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In contrast, only 33 genes are found in Nematostella and both Drosophila and C. elegans but not in any vertebrate, representing putative deuterostome or vertebrate loss, indicating a much lower degree of gene loss in the vertebrates than in the ecdysozoan model systems.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“In other studies (e.g., (42)), the effect of long branch attraction is minimized by including additional taxa that break up long branches, generating a phylogeny that agrees with our more limited taxon sampling but larger gene set.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [42]
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Nevertheless, since half of the predicted genes are in scaffolds containing 48 or more genes, the present draft assembly is sufficiently long-range to permit useful analysis of synteny with other species, as shown below.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Each family thus represents a single gene in the eumetazoan ancestor whose descendents survive in recognizable form as modern genes in both cnidarians and bilaterians.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Introns that are shared between Nematostella and vertebrates and/or other bilaterians are most parsimoniously interpreted as conserved ancient eumetazoan introns (44).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [44] source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“To overcome this limitation we developed a new method to search for statistically significant conserved linkage groups that does not rely on gene order.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although these eumetazoan gene families are conserved with other eukaryotes, animals have a unique complement due to family expansion/contraction on the eumetazoan stem.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The observation of conserved linkage groups is most easily explained as the remnants of large ancestral chromosomal segments containing hundreds of genes that have evolved without obvious constraint on gene order within each block.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Seven of the PALs link anemone scaffolds to multiple regions of the human genome in a manner consistent with multiple large-scale duplication events along the vertebrate lineage (reviewed, for example, in (53)).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [53] source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Each class of scaffolds and chromosome segments is most easily interpreted as collecting together segments of the present day Nematostella and human genomes that descend from the same chromosome of the eumetazoan ancestor, and therefore defines a putative ancestral eumetazoan linkage group (PAL).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“due to gene fusions and/or domain shuffling events on the eumetazoan stem”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“focal adhesion kinase (FAK) is targeted to focal adhesions in eumetazoans because of the addition of an animal specific focal adhesion targeting domain to the ancient kinase domain”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These seven PALs represent the ancestral (preduplication) linkage of these regions.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This is a lower bound on the true extent of the remnant ancient linkage groups, since our analysis is limited by the length of the Nematostella scaffolds and the use of conservative statistical criteria.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Further relaxing gene order constraints dramatically increases the number of such segments expected by chance, reducing the power of this approach to detect even more ancient conserved genome organization in the face of intrachromosomal rearrangements.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesNone of the sources cited for this claim have been checked yet.
In the paper
“Hox genes in Nematostella and other cnidarians are also expressed in spatial patterns consistent with an ancient role in embryonic development (54)(55)(56).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The ancestry of these genes can be traced back to the eukaryotic radiation through their ancient domains”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A general trend in the evolution of signaling pathways may have been the co-option of cytosolic signaling components into pathways that could be regulated by newly invented ligands and receptors”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes- The authors state this as an assumption: Processes conserved between living species were likely functional in their common ancestor.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The presence of essentially complete signal transduction pathways in the common gene set of cnidarians and bilaterians strongly suggests that the integration of novel eumetazoan genes into these systems was largely complete in the eumetazoan ancestor”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- The authors state this as an assumption: Processes conserved between living species were likely functional in their common ancestor.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the oldest known conserved synteny outside of prokaryotic operons”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It appears that retrotransposition of retrotransposons, despite their high diversity, has not been as efficient as propagation of DNA transposons in the anemone genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This newly acquired repertoire almost certainly plays a key role in defining vertebrates and mammals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We suggest that Tx1-like elements form a novel clade of non-LTR retrotransposons differing from the L1 clade elements by the strong target-site specificity.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“It makes Nematostella the first metazoan with Polintons constituting a substantial portion of the genome (17).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [17] source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Even this may be an overestimate, since quite a few of the genes with lower c-values are at the edges of short scaffolds, and their other half may be picked up by another scaffold, causing 2 annotations for a single gene.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“their genomes are relatively poor models for the ancestral eumetazoan genome, having lost introns, genes, and gene linkages”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The variety of different types of DNA transposons found in the anemone genome is the highest among eukaryotic species studied so far.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we estimate the loss in Nematostella since the last common ancestor (LCA) with human as 158 / (158 + 1258) = 11%.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes- The authors state this as an assumption: Intron losses have occurred independently in the human and Nematostella lineages.
- The authors state this as an assumption: The probability of independent intron insertion events at the same location is negligible.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Various ancient cytosolic proteins (talin, paxillin, Grb2, Sos and Crk) have been brought under the control of two novel receptors, integrin a and integrin b (the former being a Type I novelty and the latter a Type II novelty).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This method of counting orthologs, and this null model control naturally for independent tandem gene duplicates which could otherwise artifactually inflate the number of observed orthologs in circumstances where there is no remnant of conserved synteny, because tandem duplicates arising independently should be contained in a single reconstructed ancestral gene cluster.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
In the paper
“This suggests a considerable gain of introns in the nematodes, as also reported by [Logsdon 2004].”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
What the sources say
- Not checked yetcites Logsdon 2004
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We interpret these collections of modern sequences to be descended from the same chromosomes, or chromosomal segments of the common ancestor of eumetazoa, and refer to them therefore as putative ancestral linkage groups, or PALs.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These discontinuities are most easily explained by chromosomal fusions or large-scale re-arrangements in the human lineage which are recent compared to the time scale of gene order evolution.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A detailed look at integrin signaling (Figure5d) reveals that most of the core components of the FAK and Fyn/Shc pathways were present in the eumetazoan ancestor.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesWhat the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note the importance of the filtering out weak hits in this method, as the presence of such hits would significantly increase the false positive rate in the detection of segments of conserved linkage.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- It may state two separate claims as one. 83
- Probably not a substantial claim. 55
- The quote only partly states this claim. 5
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The total assembly spans ~357 Mb, with half of this sequence in 181 scaffolds longer than ~470 Kb.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The emerging picture is one of surprising conservation in gene content, structure, and organization between Nematostella and vertebrates, even to the point of retaining chromosome-scale gene blocks whose linkage in modern genomes has been preserved from the genome of their common ancestor.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We estimate that the Nematostella genome contains ~18,000 bona fide protein-coding genes, comparable to gene counts in other animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The depth of the Nematostella-Hydra split (comparable to the protostome-deuterostome divergence) emphasizes the distant relationship between anthozoans and hydrozoans.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Althought many eumetazoan introns are evidently of ancient eukaryotic origin (46) --for example, nearly 26% of human and Nematostella introns are conserved with Arabidopsis, and 24% with Cryptococcus --the remainder appear to be shared only by animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [46]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found 673 gene families represented in model protostomes and vertebrates, but not in Nematostella.These are candidates for bilaterian novelties.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“We also generated ~15,000 ESTs from the ctenophore (comb jelly) Mnemiopsis leidyii to attempt to place this enigmatic phylum on the tree, but could not resolve its precise phylogenetic position with significant support (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [32]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“From the shotgun assembly and the analysis of alignments between shotgun reads, we measured a rate of single nucleotide polymorphism among the four haplotypes as 0.8%, or ~1/125 bp, approximately ten times the SNP rate in the human population.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:plain· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Within alignable regions, nearly 81% of human introns are found in the same position and phase in Nematostella, and conversely 82% of the anemone introns are also found in orthologous positions in human genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Not only are the number of exons per gene similar between Nematostella and vertebrates, but the precise location and phase (i.e., the positioning of the splice sites relative to codon boundaries) of introns are also highly conserved between anemone and human.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
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In the paper
“Thus the parental anemones whose genomes we sampled have somewhat less allelic variation than broadcast spawning invertebrates such as sea squirts (~2%) (7) and sea urchins (5-10%) (8), or outbreeding plants like Populus (~2%) (34), but a comparable amount to the pufferfish (0.5%) (35).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
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In the paper
“Intron-containing genes that are descended from the ancestral eumetazoan gene set in humans and anemones have a median of ~8 and ~6 introns per gene respectively, while those from fruit fly have only ~3.(32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [32]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“1,292 eumetazoan gene families have detectable descendents in anemone and at least two of the three vertebrates, but appear to be absent in both fruit fly and soil nematode, and were therefore either lost (or were highly diverged) in both of these model protostomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“While ~22,000 of all predicted genes have a significant alignment (BLAST e-value < 1e-10) to known proteins in SwissProt/Trembl and therefore have some homology support, analysis of a random sampling of genes suggest that some of these appear to be gene fragments, possible pseudogenes, or relics of transposable elements, leading to a discounting of the true gene count to ~18,000 (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“While approximately one-third of the shotgun sequences were not assembled, they could typically be characterized as derived from long (>100 Kb) tandem-repetitive minisatellite arrays suggestive of heterochromatin, implying a total genome size of ~450 Mb (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Despite the fact that flies and nematodes share a more recent common ancestor with human than sea anemones do, we find that the anemone peptides are more similar to human than to either of the model protostomes (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [32]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In contrast, the fruit fly and nematode model systems have experienced significant gene loss, intron loss, and genome rearrangement.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
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In the paper
“Some, such as Wnt, SFRP, dpp/BMP, activin and chordin are Type I novelties with no homology to proteins from outgroups”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Caveolin, a membrane adapter that couples the integrin a subunit to Fyn is present in the Nematostella genome and is a Type I novel protein”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“These include important signaling factors, like the secreted wingless (Wnt) and fibroblast growth factor (FGF) families, and transcription factors, including the T-box and mothers-against-decapentaplegic (SMAD) families (Table 5b).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The 40 human segments that show conserved synteny with Nematostella cover half of the human genome; within such human segments, typically 40-50% of eumetazoan-derived genes have counterparts in syntenic Nematostella segments, and vice versa.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“Nematostella has several clusters of homeobox genes (56)(57)(58), but only those on scaffolds 3 and 61 are embedded within the ancestral eumetazoan Hox context, providing independent support for the assignment of these homeobox genes as bona fide Nematostella Hox genes (54,56,59).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“type II receptors turn out to be ancient eukaryotic kinase genes that were co-opted for this function”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Tetrapods have four Hox clusters that arose by duplication on the vertebrate stem --HoxA (human chromosome 7p15.2),HoxB (17q21.32),HoxC (12q13.13),and HoxD (2q31.1)--which all appear in the same eumetazoan PAL, linked to eight Nematostella scaffolds (Figure 4d).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“consist of animal genes whose domains are all ancient (i.e., each found in other eukaryotes) but which occur in apparently unique combination in eumetazoa relative to known non-animal genes (32)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“The eumetazoan genes of ancient eukaryotic ancestry are themselves descended from approximately ~5,148 eukaryotic progenitors by nearly one thousand gene duplications along the eumetazoan stem, that is, after the early radiation of eukaryotes ~1100-1500 Mya (60) but prior to the divergence of cnidarians and bilaterians (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
What the sources say
- Not checked yetcites [60] source
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Remarkably, we find that not only is the organization of the Hox cluster itself preserved, but that there is an extensive block of 225 ancestral genes (Table S7.3) that were linked to Hox in the eumetazoan ancestor and have (independently) retained that linkage in both the modern human and anemone genomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Surprisingly, despite extensive local scrambling of gene order, we find extensive conservation of synteny between the Nematostella and vertebrate genomes, allowing the identification of ancient eumetazoan linkage groups.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Alignment 1 consists of 19,563 columns, with no missing data.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We identified 809”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesThe quote only partly states this claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“There are 242 clusters of tandemly duplicated genes, comprising 2-13 members, with annotated Pfam domains, which apparently were duplicated after split of bilateria”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Troyka retrotransposons are present also in sea urchin, and the hAT5 and hAT6 transposons are wide spread in sea urchin, sea squirts and lancelet.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The large set of all predicted models was reduced to a non-redundant set of 27,273 representative models (Filtered Models), where every locus is described by a single best gene model according to the criteria of homology and EST support.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“There are 5 large clusters of short proteins (around ~100aa), each comprising 55-74 members with weak similarity to hypothetical short ORFs from fungi (28)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
What the sources say
- Not checked yetcites [28]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For Nematostella, this curve shows a large excess, exceeding the human curve for values of Cmin > 0.5, while falling below human at high Cmin values.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The five elements lacking notes are not identified by either of these methods.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Repeat sequences reconstructed from unassembled WGS reads
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“10 families of tandemly repeated sequences were identified which occur in arrays longer than fosmidlength and account for 32% of the WGS data set.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Repeat sequences reconstructed from unassembled WGS reads
Strength:plain· not yet calibratedn = 10Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“All nodes were resolved as shown in 100% of the samples trees.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Some are novel pairings of ancient domains (such as neuropilin and Lim-homeobox genes)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In addition to olfactory and taste receptors, the human genome shows strong recent preference of C2H2 zinc finger genes with a KRAB domain, keratin, and immune defence proteins.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Strength:boosted· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“we assigned GO (25) terms to 12,786 proteins, 16,625 (78%) proteins to KOG clusters (26), and 695 distinct EC numbers were assigned to 2,822 proteins mapped to KEGG pathways (27).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
What the sources say
- Not checked yetcites [25]
- Not checked yetcites [26]
- Not checked yetcites [27]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The anemone genome is also populated by a novel superfamily of eukaryotic”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Transposable elements (TEs) constitute more than 26% of the assembled sea anemone genome (Table S2.3) and belong to >500 families.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While the anemone 10,632-bp EnSpm-1_NV and 9,347-bp EnSpm-2_NV transposons encode transposases (TPase) similar to the plant En/Spm TPase and are flanked by 3-bp targets site duplications typical for known En/Spm elements”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of these, the first had the highest likelihood score, but it was not significantly better than the second in a Shimodaira-Hasegawa test.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
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In the paper
“the anemone genome contains several families of RTE-like elements, RTEX in Fig. S2.1, which are longer than canonical RTE elements and contain an additional ORF at their 5' terminal portion that codes for the esterase domain, analogously to elements from the CR1/L2 clade (20).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [20] source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Certain enzymes important in synaptic transmission (e.g.DOPA-beta monooxygenase) and some vesicular trafficking proteins (e.g.synaptophysin) appear as completely novel (Type I) eumetazoan proteins”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“others are novel animal genes (e.g., Hes, Gcm, netrin, semaphorins, dachsund)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There are 9 neurotoxins genes, with an anemone neurotoxin domain (PF0076) previously found only in the Cnidaria, but not previously in Nematostella, and 5 copies of green fluorescent protein (PF01353), originally found in jellyfish and predominantly found in Cnidaria.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“146,095 ESTs were clustered into 30,813 consensus sequences and both individual ESTs and consensus sequences were mapped onto genome assembly using BLAT (10).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
What the sources say
- Not checked yetcites [10] source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The genome of Nematostella vectensis includes 27,273 predicted gene models built using the JGI Annotation Pipeline, described below.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Alignment 2 consists of 19,977 columns, however only 2272 columns contain Mnemiopsis sequence.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The complete set of these numbers of shared orthologous genes are shown in figure S7.3, for all scaffolds (67/147) and segments (40/98) which participated in a statistically significant shared synteny relationship.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Table S7.3 has 112 yellow cells, corresponding to 112 cases of statistically significant conservation of synteny between a Nematostella scaffold and a segment of the human genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In 2,347 cases, a human gene was found to have a mutual best hit to both a Nematostella and an Arabidopsis gene, forming a tentative cluster of orthologous genes to be studied further.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For human-Nematostella, we found no strict significant conservation of gene order, but by choosing a large value of Nmax we nonetheless detect regions of conserved linkage in which the local gene order has been scrambled.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The rows and columns of this table have been ordered to reveal 13 sets of scaffolds and chromosome segments, defined by the criterion that none can be subdivided without separating into different sets a scaffold-segment pair with significant evidence (p<0.01) for conserved synteny.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we find 26.5% of all Nematostella introns and 26.1% of all human introns are shared with Arabidopsis”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The rate of single nucleotide polymorphism observed in the assembled genome sequence is 0.8%.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Figure S2.1: Observed density of polymorphic sites
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nematostella has the most introns at these conserved positions, followed by human with a relative intron frequency of about 0.91, whereas nematode and in particular fly have considerably fewer introns (0.37 and 0.21).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Using Nmax = 40 and considering only segments of 9 or more participating genes, we find 33 such segments of conserved synteny between human and Nematostella, with none expected by chance, as seen by running the algorithm on the scrambled set.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Table S7.X lists the 255 ancestral gene clusters linked with the HOX clusters in PAL-A.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“At this stage we were left with 11,351 pairwise hits, involving 6,986 nematostella genes and 8,426 human genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The conclusion is that 2N = 30, the same number as in Hydra.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The genes of the HOX C cluster fall into such a large family, but have been labeled to show the position of the HOX cluster.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“integrin a and integrin b (the former being a Type I novelty and the latter a Type II novelty).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that the nematode, although having retained only ~23% of the introns since the LCA with human have ~37% of the number of human introns.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“The other Cnidarian classes are united by their pelagic medusae and uniquely linear mitochondrial genomes (9) into the Medusozoa, including Hydra and related hydroids, jellyfish, and box jellies.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [9] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Similarly, we can characterize the genome of this long-dead eumetazoan progenitor by comparing modern DNA and protein sequences and identifying conserved features in different modern lineages.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“To probe the ancestral eumetazoan genome requires sequences from even deeper branches of the animal tree, comparing bilaterian and non-bilaterian phyla.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Some of the oldest animal body fossils (e.g., the Ediacaran Charnodiscus (10) but see also (11,12)) and fossil embryos (13) are plausibly relics of stem cnidarians, suggesting a Precambrian origin for the phylum.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“This eumetazoan ancestor lived perhaps seven hundred million years ago, but is not preserved in the fossil record (3).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [3]
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Comparisons (4-6) between fruit fly, nematode, and vertebrate genomes reveal greater genomic complexity in the vertebrates (and other deuterostomes (7,8)) as measured by gene content and structure, but at the same time show that many genes and networks are shared across bilaterians.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Among Anthozoan cnidarians, the starlet sea anemone Nematostella vectensis is an emerging model system (14,15).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [15]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Our ability to recognize ancient genomic features depends on the availability of sequences from diverse living animals, and can only illuminate genomic characteristics that have an intrinsically slow rate of change and/or are preserved by selective pressures.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“This estuarine burrowing anemone is found on the Atlantic and Pacific coasts of North America, as well as the coast of southeast England (16) (Figure 1).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [16]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Comparison of Nematostella genes to those of other animals reveals that the ancestral eumetazoan genome must have been intron-rich, with gene structures closely resembling those of modern vertebrate and anemone genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“The source population for the genome sequence (Rhode River, Maryland) appears typical in this regard (37).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [37] source
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Nematostella cultures are easily maintained in the laboratory.With separate sexes, inducible spawning, and external fertilization (14,17), embryos are available throughout the year.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [17]
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The relatively low level of intra-specific genetic variation in Nematostella vs. marine broadcast spawners might be explained if its estuarine habitat limited gamete dispersal and led to a smaller efective population size.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This is of course only a very rough estimate with numerous caveats, most notably that there is no guarantee that the rate of protein evolution was constant on the eumetazoan stem, but provides a rough time scale for the eumetazoan radiation.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Rests on an assumption: The rate of protein evolution was constant on the eumetazoan stem for the molecular clock estimate.
In the paper
“To avoid contamination from commensal microbes common to adult anemones and minimize the impact of haplotypic variation, we prepared genomic DNA from the larvae of a single mating pair originally isolated from the same lagoon (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
In the paper
“Genetic fingerprinting of wild Nematostella populations indicates a high degree of genetic structuring at fine spatial scales, implying extremely low levels of gene flow between neighboring estuaries (36).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [36]
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Currently there are no physical or genetic maps of Nematostella, so we could not reconstruct the genome as chromosomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The egg mass may be a derived feature of Nematostella that is related to its colonization of the estuarine environment.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Analysis of the Nematostella genome in the context of sequences from other eukaryotes reveals the genomic complexity of this last common cnidarian-bilaterian ancestor, and begins to illuminate the rich history of genes and gene networks already present at the base of the animal tree of life.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Intron conservation can be unambiguously assessed by identifying well-aligned regions of orthologous proteins that are interrupted by introns in one or more species (Figure 3a).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This supports the paleontological evidence that the radiation of the cnidarian phylum is quite ancient, and suggests that significant variation in gene content and gene family diversity may be found when the anemone genome is compared with that of the hydrozoan Hydra.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Between animal phyla, however, no significant large-scale conserved synteny has been identified, suggesting that signals of the ancestral eumetazoan genome organization were erased by subsequent chromosomal breaks and translocations along the various lineages.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Cell-cell adhesion mediated by cell-ECM interactions is a hallmark of animal multicellularity (63)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
What the sources say
- Not checked yetcites [63]
Strength:boosted· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Animals rely on cell-cell signaling for cellular coordination during and after development (64)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
What the sources say
- Not checked yetcites [64] source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These are evidently members of ancient eukaryotic gene families that were already established in the unicellular ancestors of the metazoa, and are involved in core eukaryotic cellular functions including amino acid, carbohydrate, and lipid metabolism; small molecule and ion transport; DNA replication, core transcriptional machinery, RNA processing, and translation; intracellular vesicular Traffick”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The human genome was selected as a reference since it is known to have a slow rate of chromosome evolution relative to other mammals (52), and has preserved chromosomal segments relative to teleost fish (48).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [52]
- Not checked yetcites [48]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“In Bilateria, the integrin pathway mediates signaling from the extracellular matrix (ECM) that elicits various responses to modulate cell adhesion, motility, and the cell cycle”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
What the sources say
- Not checked yetcites Giancotti and Caveolin
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“to generate organismal novelty such new genes must be integrated with other novel and existing genes to evolve expanded or modified biochemical pathways and/or regulatory networks”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Eumetazoan networks and pathways
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“We can rule out ancient loss in the protostome lineage based on the results of Raible et al. (2005) for Platynereis, which in combination with our analysis shows that the ancestral protostome genome was also intron-rich.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites Raible et al. (2005)
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Conserved linkage groups representing ancestral vertebrate chromosomes can be defined by comparing fish and mammalian genomes and genetic maps, despite the presence of only modest segments of conserved gene order (48,49).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [48]
- Not checked yetcites [49] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Thus assuming ~8 introns per ancestral gene, ~1 novel intron has been introduced in a typical modern animal gene since the eumetazoan radiation, a rate of approximately ~10 -9 introns/gene/year, which is comparable to the rate of nucleotide substitution and gene duplication (47).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [47]
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Five PALs link Nematostella scaffolds to single human chromosome regions, which suggests that the vertebrates specific duplicates of these segments have been lost or fused and dispersed among other chromosomes (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We cannot rule out the possibility, however, that such apparently animal-specific introns were in fact present in the last common ancestor of plants, fungi, and animals, but were convergently lost in both plants and fungi.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Similarly, limited conservation of synteny is recognizable within insects (e.g., between flies and bees (50)).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [50] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The surprising extent of this conserved linkage suggests that either the neutral rate of inter-chromosomal translocations is low (on the order of a few breaks/fusions per chromosome since the eumetazoan ancestor, excluding intra-chromosomal rearrangements), or that selection has acted to maintain linkage of large groups of genes for unknown reasons.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Modern animal genomes retain features inherited from the eumetazoan ancestor that have been elaborated on, and sometimes overwritten by, subsequent evolutionary elaborations and simplifications”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: Processes conserved between living species were likely functional in their common ancestor.
None of the sources cited for this claim have been checked yet.
In the paper
“We see from Figure 2b that the cnidarian-bilaterian split lies ~30% of the way between these two nodes (adopting the midpoint rooting as shown), suggesting that the eumetazoan ancestor lived between 670 and 820 Mya.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“gene regulatory changes can also play a central role in generating novelties, allowing co-option of ancestral genes and networks to new functions (67)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
What the sources say
- Not checked yetcites [67]
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We compared the results obtained with this set with those obtained using Nematostella rather than human as the anchor for identifying orthologs, and found that it did not change the results.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“All known RTE elements, including those in plants, insects, nematodes, and vertebrates, contain only one ORF and are characterized by extremely frequent 5' truncations of the RTE elements during their retrotransposition.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [19]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Among DNA transposons, the hAT superfamily is well-known for TSDs that are always 8 bp long (14).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
Strength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“these may have arisen by sequence divergence from ancient eukaryotic genes, but the trail is obscured by deep time”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“FGENESH was trained on this set to achieve sensitivity and specificity of 81% and 80%, respectively.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Multiple runs from different starting topologies all converged on the same topology, branch lengths and posterior probabilities for protein evolution model parameters within approximately 10,000 monte carlo iterations.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“all known LTR retrotransposons, including retroviruses, are defined by 4-6 bp TSDs (14).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that this analysis is biased towards vertebrates, for which more domains have been characterized.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This approach enriches the set for orthologous gene pairs while removing weak super-family similarities from the analysis.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Since we compared 147 scaffolds with 98 segments, we applied a Bonferroni correction factor of 1/14406.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These large genes families are more likely to have members showing spurious conserved synteny, since they may have members in many regions of the genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The number of chromosomes was determined by analysing over 90 metaphase plates in spreads.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which translate into maximum intron gains of ~9% in human and ~7% in Nematostella.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In a similar fashion, we estimate a loss of almost 22% along the human lineage, twice the amount of introns lost in the Nematostella lineage.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: Intron losses have occurred independently in the human and Nematostella lineages.
- The authors state this as an assumption: The probability of independent intron insertion events at the same location is negligible.
In the paper
“The parsimony assignment of characters to internal nodes is independent of this gain/loss weight ratio.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Methods for Intron Gain/Loss tree
What the sources say
- Not checked yetcites [40]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: The phylogenetic topology onto which intron characters were projected is correct.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that this method does not require strict conservation of gene order: inversions on scales smaller than Nmax are tolerated.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“For both Panther Pathways and Pather Ontology, we limited our tests to the 100 ontology terms which had the greatest number of inferred ancestral genes assigned to them, and applied a Bonferroni correction for 100 tests, even though this is somewhat conservative, since the categories have significant overlap.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Functional annotation of ancestral gene clusters
What the sources say
- Not checked yetcites [44]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“After traversing all alignments, we have a set of conserved regions, on which we can impose a minimum member limit (typical 3 pairs) to remove potentially spurious regions.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“From these numbers we estimate the intron losses in fly, nematode, and human since their LCA to be 82% , 77%, and 12% respectively.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“In order to detect the significance of these regions, we randomly scrambled the order of the genes on each chromosome or scaffold and applied, for the same sequence alignment data, the algorithm to the scrambled data set.This allows us to choose parameters to minimize false positive detection.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To the extent that the introns in highly conserved peptide regions studied here are representative of introns in general, the above analysis suggests that the Nematostella genome has only lost 11% of its introns since the LCA with human, and gained at most 7%.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: The introns in highly conserved peptide regions studied are representative of introns in general.
The paper relies on this without support.
The rate of protein evolution was constant on the eumetazoan stem for the molecular clock estimate.
“there is no guarantee that the rate of protein evolution was constant on the eumetazoan stem”
The paper relies on this without support.
The null model in which scaffolds and human segments have gene content independently drawn from the ancestral set is appropriate for testing conserved linkage.
“This number of shared orthologous genes was compared to a null model in which the scaffolds and segments have gene content independently drawn from the ancestral set.”
The authors state this as an assumption.
Processes conserved between living species were likely functional in their common ancestor.
“using the basic principle of evolutionary developmental biology: processes that are conserved between living species were likely functional in their common ancestor”
The paper relies on this without support.
The eumetazoan ancestor was the progenitor of all extant animals with nervous systems.
“The eumetazoan ancestor was the progenitor of all extant animals with nervous systems”
The paper relies on this without support.
Present-day cnidarians lack a clear mesoderm.
“present-day cnidarians lack a clear mesoderm”
The paper relies on this without support.
Many genes involved in mesoderm development are associated with basic patterning and/or regulation of cell migration and fate.
“many of these genes are associated either with basic patterning functions and/or the regulation of cell migration and fate”
The paper relies on this without support.
Cnidarians and ctenophores are the earliest branching metazoan phyla with a nervous system.
“Cnidarians and ctenophores are the earliest branching metazoan phyla that have a nervous system”
The authors state this as an assumption.
The estimates of tandem array sizes depend on normal cloning behavior for repetitive sequences.
“These estimates depend on the assumptions of”
The authors state this as an assumption.
Any gene has an equal probability of getting duplicated and fixed in the population.
“We then formulated a neutral-evolution hypothesis that any gene has an equal probability of getting duplicated and fixed in the population.”
The authors state this as an assumption.
Intron losses have occurred independently in the human and Nematostella lineages.
“Assuming that intron losses have occurred independently in the human and nematostella lineages”
The authors state this as an assumption.
The probability of independent intron insertion events at the same location is negligible.
“and that the probability of independent intron insertion events at the same location is negligible”
The authors state this as an assumption.
The introns in highly conserved peptide regions studied are representative of introns in general.
“To the extent that the introns in highly conserved peptide regions studied here are representative of introns in general”
The paper relies on this without support.
The phylogenetic topology onto which intron characters were projected is correct.
“projecting these characters onto the (known) topology.”
The authors state this as an assumption.
The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
“a null model in which scaffolds and segments comprise genes descending from genes drawn independently from the set of 7,766 ancestral genes.”
The authors state this as an assumption.
The centroid sequence is a surrogate for the peptide sequence ancestral to each orthologous cluster.
“This provides a surrogate for the peptide sequence that is ancestral to each cluster.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Cnidarians seem to possess almost the complete bilaterian regulatory gene tool kit, including anterior and posterior hox genes (Finnerty et al. 2004; Putnam et al. 2007) and generate many of the ectodermal, neuronal, endodermal, and mesodermal differentiated cell types also found in bilaterians.”
From An integrated view of precambrian eumetazoan evolution (2009) · cites this paper as Putnam et al. 2007
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning the divergence between cnidarians, chordates, sponges, and placozoans”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [40]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“in development of the most basal cnidarian clade, anthozoans, regulatory genes are expressed in bilateral axial patterns that indicate an underlying set of bilateral regulatory states.”
From An integrated view of precambrian eumetazoan evolution (2009) · cites this paper as Putnam et al. 2007
The cited source says what the claim attributes to it.
In the citing paper
“Genome sequences of some animal clades very distantly related to humans, including sponges (37), placozoans (flat animals) (38), and cnidarians (i.e., true jellyfish, corals) (39, 40), suggested that many genes thought to define vertebrates were, in fact, present even in earlier ancestral animals”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [40]
In the citing paper
“The publication of several cnidarian genomes has shown that much of the molecular architecture underlying neurogenesis and neuron functioning is conserved between bilaterians and cnidarians [17,47–51].”
From Evolution of eumetazoan nervous systems: insights from cnidarians (2015) · cites this paper as [17]
In the citing paper
“The sequencing in recent years of the whole genome of different cnidarian species, most notably those of the anthozoan Nematostella vectensis and the hydrozoan Hydra magnipapillata (Figure 1) [50,51], has offered the exciting possibility to quickly gather an overview on the entire complement of receptors in these species.”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [50]
In the citing paper
“Reflecting this ancestral core, cnidarian genes are often more similar to vertebrate genes than vertebrate genes are to those of more diverged animals like Caenorhabditis or Drosophila [50,109].”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [50]
In the citing paper
“Morphological and phylogenetic evidence makes the cnidarian polyps an ideal proxy to the 'prebilaterian eumetazoan' body organization, and cnidarian model systems reveal evolutionary ancestry of bilaterian characters 15,16 .”
From Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans (2014) · cites this paper as [16]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Intron analysis gives two sample sizes
MajorThe main-text figure description reports 5,175 introns for the seven-species analysis, whereas the methods report 4,342 introns at the same 2,645 aligned positions across seven genomes.
“Based on a sample of 5175 introns at highly conserved protein sequence positions from Arabidopsis thaliana (Plant), Crytococcus neoformans (Fungus), C. elegans (Nematode), D. melanogaster (Fly), Ciona intestinalis (Sea squirt), Homo sapiens (Human), and Nematostella (32).”
“4342 introns from the seven genomes at 2645 aligned positions which contain an intron in at least one of the seven orthologs.”
Hox-linked ancestral cluster count differs
MinorThe text and the Table S7.3 caption give 225 ancestral genes or clusters linked to the Hox region, but a supplemental description gives 255 for that linkage group.
“there is an extensive block of 225 ancestral genes (Table S7.3) that were linked to Hox in the eumetazoan ancestor”
“Table S7.X lists the 255 ancestral gene clusters linked with the HOX clusters in PAL-A.”
Supplement assigns two different contents to Table S7.3
MinorOne passage describes Table S7.3 as a colored synteny grid with 112 significant cells; its caption instead identifies it as a list of 225 Hox-linked ancestral gene clusters.
“Table S7.3 has 112 yellow cells, corresponding to 112 cases of statistically significant conservation of synteny between a Nematostella scaffold and a segment of the human genome.”
“Table S7.3:The 225 ancestral gene clusters linked with the HOX clusters in PAL-A:”
Table S7.2 is described as both complete and limited to three groups
MinorThe text says Table S7.2 shows all 13 ancestral linkage groups, while its caption says the grid covers only groups A, B, and C.
“The complete Oxford grid showing all 13 PALs is shown in Table S7.2.”
“Table S7.2:Complete Oxford Grid for Human-Nematostella comparison "Oxford grid" which tabulates the number of ancestral gene clusters shared between the 22 Nematostella scaffolds (columns) and 14 segments of the human genome (rows) that are assigned to PALs A, B and C.”
KOG annotation percentage uses an inconsistent denominator
MinorThe stated 16,625 KOG-assigned proteins are 61.0% of the 27,273 representative models, not 78%. No alternative denominator is identified for this percentage.
Reported 78 · recomputed 60.957724
“For this set of representative gene models we assigned GO (25) terms to 12,786 proteins, 16,625 (78%) proteins to KOG clusters (26), and 695 distinct EC numbers were assigned to 2,822 proteins mapped to KEGG pathways (27).”
Citations
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A genomic perspective on protein families.
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Comparative Genomics of the Eukaryotes
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Self-citation(2007) · Wiley eBooks · doi:10.1128/9781555817954 · Cited by 1,311
Flagged first, then by citations
1 of the 71 references couldn’t be matched to a known paper.
Research works printed but not linked: 3
- C. Nielsen, in Animal Evolution (Oxford Univ. Press, Oxford, ed. 2, 2001), pp. 51–58.
- J. C. Sullivan, A. M. Reitzel, J. R. Finnerty, Genome Informatics17, 219 (2006).
- J. S. Conery, M. Lynch, Pac. Symp. Biocomput.2001, 167 (2001).
Cited by
Sorted by citations
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Chalhoub, B., Denœud, F., Liu, S., Parkin, I. A. P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., et al. (2014) · Science · doi:10.1126/science.1253435 · Cited by 2,514
The amphioxus genome and the evolution of the chordate karyotype
Putnam, N. H., Butts, T., Ferrier, D. E. K., Furlong, R. F., Hellsten, U., Kawashima, T., Robinson‐Rechavi, M., Shoguchi, E., Terry, A., Yu, J., et al. (2008) · Nature · doi:10.1038/nature06967 · Cited by 1,595
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Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D., & Peterson, K. J. (2011) · Science · doi:10.1126/science.1206375 · Cited by 1,336
Overview of the Matrisome--An Inventory of Extracellular Matrix Constituents and Functions
Hynes, R. O., & Naba, A. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a004903 · Cited by 1,349
Metadata
- Authors
- Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., Jurka, J., Genikhovich, G., Grigoriev, I. V., Lucas, S. M., Steele, R. E., Finnerty, J. R., Technau, U., Martindale, M. Q., & Rokhsar, D. S.
- Affiliations
- Genetic Information Research Institute (US)
- Corresponding author
- Rokhsar, Daniel S.
- ORCID
- Venue
- Science
- Published
- 2007-07-06
- Volume
- 317
- Issue
- 5834
- Pages
- 86-94
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2067558229
- Semantic Scholar
- 0b61b3a2a55b156bb026a4c83d26d9b95c5af753
- Cited by
- 1,555
- References
- 71
- Citations by year
- 2026: 27 · 2025: 30 · 2024: 52 · 2023: 48 · 2022: 66 · 2021: 49 · 2020: 73 · 2019: 72 · 2018: 84 · 2017: 81 · 2016: 89 · 2015: 97 · 2014: 89 · 2013: 83 · 2012: 110
- FWCI
- 103.09
- Type
- journal article
- Language
- en
- Open access
- green
- www.osti.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- Funders
- U.S. Public Health Service (THL007279F)
- U.S. National Library of Medicine (P41LM006252)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- Nematostella vectensis, Cnidaria, genome evolution, gene repertoire, exon-intron structure, genetic linkage, comparative genomics, signal transduction, adhesion, synaptic transmission, animal evolution
- MeSH terms
- Animals, Cell Adhesion, Biological Evolution, Genes, Multigene Family, Humans, Introns, Genetic Linkage, Muscles, Nervous System Physiological Phenomena, Phylogeny, Sea Anemones, Signal Transduction, Genome, Human, Genome, Sequence Analysis, DNA, Evolution, Molecular, Genomics, Synteny, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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